Heatmap and rna-seq
Hello everyone!
I have a list of pathways from GSEA analysis (RNA-Seq data) and I want to plot a heatmap of genes associated with pathways, showing distinctly each pathway in the heatmap. Can somebody help me with this
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dsull
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qudrat.nii •
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qudrat.nii •
3 answers
install.packages("pheatmap")
library(pheatmap)
setwd("/Users/data_analysis/results")
data <- read.table(file = "log2cpm.tsv", header = T, sep = "\t")
pheatmap(mat = data)
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pinheirofabiano •
https://maayanlab.cloud/clustergrammer/
It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pathway x gene matrix or a sample x gene matrix.
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap.
You have not indicated that you require assistance with coding; so, I will end my answer right here.
Kevin
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Kevin Blighe
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